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comparison mlmm/source_library/plot_MLMM.Ago.r @ 0:6b7107812931 draft

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author dereeper
date Thu, 02 Jul 2015 05:42:38 -0400
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-1:000000000000 0:6b7107812931
1 ## fonction ###########################################################################
2 plot_MLMM.Ago<-function(x) {
3 output1 <-x$out[order(x$out$Pos),]
4 output_ok<-output1[order(output1$Chr),]
5
6 maxpos<-c(0,cumsum(as.numeric(aggregate(output_ok$Pos,list(output_ok$Chr),max)$x+max(cumsum(as.numeric(aggregate(output_ok$Pos,list(output_ok$Chr),max)$x)))/200)))
7 plot_col<-rep(c('gray10','gray60'),ceiling(max(unique(output_ok$Chr))/2))
8 # plot_col<-c('blue','darkgreen','red','cyan','purple')
9 size<-aggregate(output_ok$Pos,list(output_ok$Chr),length)$x
10 a<-rep(maxpos[1],size[1])
11 b<-rep(plot_col[1],size[1])
12 for (i in 2:max(unique(output_ok$Chr))){
13 a<-c(a,rep(maxpos[i],size[i]))
14 b<-c(b,rep(plot_col[i],size[i]))}
15
16 output_ok$xpos<-output_ok$Pos+a
17 output_ok$col<-b
18 output_ok$col[output_ok$mk=='qtl']<-'cyan'
19 output_ok$col[output_ok$SNP %in% x$cof]<-'red'
20
21 d<-(aggregate(output_ok$xpos,list(output_ok$Chr),min)$x+aggregate(output_ok$xpos,list(output_ok$Chr),max)$x)/2
22
23 plot(output_ok$xpos,-log10(output_ok$pval),col=output_ok$col,pch=20,ylab='-log10(pval)',xaxt='n',xlab='chromosome')
24 axis(1,tick=FALSE,at=d,labels=c(1:max(unique(output_ok$Chr))))
25 xline(output_ok$xpos[output_ok$mk=='qtl'], col='cyan', lwd=0.1)
26 abline(h=x$bonf_thresh,lty=3,col='black')
27
28
29 if (length(output_ok$pval[-log10(output_ok$pval) > x$bonf_thresh]) > 0) {
30 text(output_ok$xpos[-log10(output_ok$pval) > x$bonf_thresh], -log10(output_ok$pval[-log10(output_ok$pval) > x$bonf_thresh]), output_ok$SNP[-log10(output_ok$pval) > x$bonf_thresh], pos=3, cex=0.7)
31 legend("topright", lty=3, paste("bonf thresh :", x$bonf_thresh ,sep=" "))
32 } else {
33 legend("topright", lty=3, paste("bonf thresh :", x$bonf_thresh ,sep=" "))
34 }
35
36 }